The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SAMPLE_PAIRED_END_1_1)'
Caused by:
Process `NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM (SAMPLE_PAIRED_END_1_1)` terminated with an error exit status (1)
Command executed:
INDEX=`find -L ./ -name "*.amb" | sed 's/\.amb$//'`
bwa-mem2 \
mem \
\
-t 2 \
$INDEX \
Bpacificus-ATCC10987-rep1-sWGS-MiSeqi100-241111_S1_L001_R1_001.fastq.gz Bpacificus-ATCC10987-rep1-sWGS-MiSeqi100-241111_S1_L001_R2_001.fastq.gz \
| samtools sort -@ 2 -o SAMPLE_PAIRED_END_1_1.bam -
cat <<-END_VERSIONS > versions.yml
"NFCORE_SEQINSPECTOR:SEQINSPECTOR:BWAMEM2_MEM":
bwamem2: $(echo $(bwa-mem2 version 2>&1) | sed 's/.* //')
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Looking to launch executable "/opt/conda/bin/bwa-mem2.sse42", simd = .sse42
Launching executable "/opt/conda/bin/bwa-mem2.sse42"
-----------------------------
Executing in SSE4.2 mode!!
-----------------------------
* SA compression enabled with xfactor: 8
* Ref file: ./genome.fa
* Entering FMI_search
ERROR! Unable to open the file: ./genome.fa.bwt.2bit.64
[W::hts_set_opt] Cannot change block size for this format
samtools sort: failed to read header from "-"
Work dir:
/Users/agrimabhatt/seqinspector/work/d0/4c595c9b0edfe8a64a1469cacb13c0
Container:
community.wave.seqera.io/library/bwa-mem2_htslib_samtools:e1f420694f8e42bd
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
nextflow run main.nf -profile test,docker --input /Users/agrimabhatt/pipeline/testdata/testdata/Miseq_PairedEnd/samplesheet.csv --outdir result_test --bwa_index /Users/agrimabhatt/seqinspector/result/bwamem2_index/bwamem2/ -with-report
51ae67c7a1786a7937e7c520871990bdb0c36634-5b3a-4877-8ce8-9ddc72aa08b5These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.